Code

Java (multiple tools) -Xmx parameter#204

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Merged

dlaehnemann merged 64 commits intosnakemake:mastersnakemake/snakemake-wrappers:masterfrom tdayris:picard_memorytdayris/snakemake-wrappers:picard_memoryCopy head branch name to clipboardNov 12, 2020

+524-94

Commits

Commits on Sep 21, 2020

• [fix] (template): Missing code in wrappers' doc. Error snakemake#187

  

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• [dev] (Picard): Memory

  

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Commits on Sep 22, 2020

• [dev] (applybqsr): Automatic Xmx fill

  

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• [dev] (baserecal): Automatic Xmx fill

  

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• [dev] (baserecalspark): Automatic Xmx fill

  

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• [dev] (combinegvcf): Automatic Xmx fill

  

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• [dev] (genotypegvcfs): Automatic Xmx fill

  

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• [dev] (haplotypecaller): Automatic Xmx fill

  

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• [dev] (selectvariants): Automatic Xmx fill

  

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• [dev] (splitncigarreads): Automatic Xmx fill

  

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• [dev] (variantfiltration): Automatic Xmx fill

  

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• [dev] (variantrecalibrator): Automatic Xmx fill

  

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• [dev] (snpsift_annotate): Automatix Xmx fill

  

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• [dev] (snpsift_dbnsfp): Automatic Xmx fill

  

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• [dev] (snpsift): genesets, gwascat and varType: automatic Xmx fill

  

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• [dev] (trinity): Aotumatix Xmx fill

  

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• [dev] (Mutect2): Java options added, with automatic Xmx fill

  

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Commits on Sep 25, 2020

• [fix] (Picard): Test if -Xmx was not set before

  

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Commits on Oct 13, 2020

• Merge branch 'master' into picard_memory

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Commits on Oct 19, 2020

• [dev] (SnpEff): Automatic Xmx fill

  

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• [dev] (SnpEff): Automatic Xmx fill in download wrapper

  

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• [dev] (Jannovar): Automatic Xmx fill

  

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• [dev] (Varscan): Automatic Xmx fill

  

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• [dev] (trimmomatic): Automatic Xmx fill

  

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• Merge branch 'picard_memory' of https://github.com/tdayris/snakemake-wrappers into picard_memory

  

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Commits on Oct 20, 2020

• [dev] (gatk4): Update with comments from @dlaehnemann and java_tmp

  

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• [dev] (jannovar): Update with comments from @dlaehnemann and java temp

  

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• [dev] (picard): AddOrReplaceGroups updated, missing test added.

  

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• [dev] (picard): Update with comments from @dlaehnemann and java temp

  

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• [dev] (collecttargetedpcametrics): Updated and missing test added

  

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• [dev] (snpeff): Update with comments from @dlaehnemann and java temp

  

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• [dev] (snpsift): Update with comments from @dlaehnemann and java temp

  

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• e[dev] (trimmomatic): Updatr with comments from @dlaehnemann, javatemp

  

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• [dev] (trinity): Update with comments from @dlaehnemann

  

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• [dev] (varscan): Update with comments from @dlaehnemann and java temp

  

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• [fix] (black): Files now blacked

  

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• [doc] (varscan): Snakefiles updated

  

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• [fix] (varscan): Test for varscan somatic had a wrong name

  

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• [doc] (trimmomatic): Snakefiles updates

  

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• [fix] (Trinity): Missing whitespace

  

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• [fix] (Trinity): Missing whitespace

  

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• [doc] (Snpsift): Snakefiles updated

  

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• [doc] (Snpeff): Snakefiles updated

  

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• [fix] (snpeff-download): Useless extra parameters removed

  

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• [doc] (picard): Snakefiles updated

  

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• [doc] (GATK): Snakefiles updated

  

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Commits on Nov 2, 2020

• [dev] (GATK4): Update with snakemake-wrappers-utils

  

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• [dev] (GATK3): Update with snakemake-wrappers-utils

  

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• [dev] (Jannovar): Update with snakemake-wrappers-utils

  

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• [dev] (Picard): Update with snakemake-wrappers-utils

  

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• [dev] (SnpEff): Update with snakemake-wrappers-utils

  

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• [dev] (SnpSift): Update with snakemake-wrappers-utils

  

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• [dev] (Trimmomatic): Update with snakemake-wrappers-utils

  

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• [dev] (Varscan): Update with snakemake-wrappers-utils

  

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Commits on Nov 12, 2020

• [fix] (NameError): snakemake-wrapper-utils updated

  

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• [doc] (Documentations): Links to todumentation added

  

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• [fix] (Black): Formatting error fixed

  

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• [fix] (SyntaxError): trailing quote removed

  

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• fix] (SyntaxError): Starting quote removed

  

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• [fix] (KeyError): missing extra definition

  

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• add mem_gb spec explanation comment in bio/jannovar/test/Snakefile

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• [dev] (gatk3): Snakefile resources specifications

  

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• Merge branch 'picard_memory' of https://github.com/tdayris/snakemake-wrappers into picard_memory

  

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• [fix] (gatk3): Removing trailing comma

  

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